Variant report

Variant	rs11712713
Chromosome Location	chr3:160852471-160852472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160838900..160841053-chr3:160850785..160853337,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10154889	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs10433352	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11717272	0.82[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720263	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11922957	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11922959	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488878	0.88[CEU][hapmap]
rs13060601	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13061088	0.81[ASN][1000 genomes]
rs13062651	0.81[EUR][1000 genomes]
rs13071892	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085336	0.83[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs13256	0.82[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599388	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16831796	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs16831886	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014810	0.84[EUR][1000 genomes]
rs34221255	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34630898	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35914913	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4494975	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4521287	0.82[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4856700	0.81[CEU][hapmap]
rs57145341	0.84[EUR][1000 genomes]
rs6441362	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772723	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs6794882	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6799805	0.87[CEU][hapmap]
rs68166680	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73021215	0.80[AMR][1000 genomes]
rs73023235	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7610432	0.84[EUR][1000 genomes]
rs7618924	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622060	0.87[CEU][hapmap]
rs7628389	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs898677	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9857855	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9876142	0.82[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs9883566	0.82[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv963285	chr3:160848780-160856433	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712713	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs11712713	SPTSSB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160844600-160859000	Weak transcription	Left Ventricle	heart
2	chr3:160850400-160882400	Weak transcription	Ovary	ovary

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